Job ID = 7114441 SRX = SRX8462198 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-07-22T05:57:03 prefetch.2.10.7: 1) Downloading 'SRR11915657'... 2020-07-22T05:57:03 prefetch.2.10.7: Downloading via HTTPS... 2020-07-22T05:58:46 prefetch.2.10.7: HTTPS download succeed 2020-07-22T05:58:46 prefetch.2.10.7: 'SRR11915657' is valid 2020-07-22T05:58:46 prefetch.2.10.7: 1) 'SRR11915657' was downloaded successfully 2020-07-22T05:58:46 prefetch.2.10.7: 'SRR11915657' has 0 unresolved dependencies Read 6300486 spots for SRR11915657/SRR11915657.sra Written 6300486 spots for SRR11915657/SRR11915657.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:27 6300486 reads; of these: 6300486 (100.00%) were paired; of these: 914025 (14.51%) aligned concordantly 0 times 4569369 (72.52%) aligned concordantly exactly 1 time 817092 (12.97%) aligned concordantly >1 times ---- 914025 pairs aligned concordantly 0 times; of these: 43628 (4.77%) aligned discordantly 1 time ---- 870397 pairs aligned 0 times concordantly or discordantly; of these: 1740794 mates make up the pairs; of these: 1607260 (92.33%) aligned 0 times 96773 (5.56%) aligned exactly 1 time 36761 (2.11%) aligned >1 times 87.24% overall alignment rate Time searching: 00:05:27 Overall time: 00:05:27 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_sort_core] merging from 8 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 2156114 / 5426530 = 0.3973 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Jul 2020 15:08:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8462198/SRX8462198.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8462198/SRX8462198.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8462198/SRX8462198.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8462198/SRX8462198.bam'] # control file = None # effective genome size = 1.21e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Wed, 22 Jul 2020 15:08:33: #1 read tag files... INFO @ Wed, 22 Jul 2020 15:08:33: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 15:08:40: 1000000 INFO @ Wed, 22 Jul 2020 15:08:46: 2000000 INFO @ Wed, 22 Jul 2020 15:08:53: 3000000 INFO @ Wed, 22 Jul 2020 15:08:59: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Jul 2020 15:09:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8462198/SRX8462198.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8462198/SRX8462198.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8462198/SRX8462198.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8462198/SRX8462198.bam'] # control file = None # effective genome size = 1.21e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Wed, 22 Jul 2020 15:09:03: #1 read tag files... INFO @ Wed, 22 Jul 2020 15:09:03: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 15:09:06: 5000000 INFO @ Wed, 22 Jul 2020 15:09:11: 1000000 INFO @ Wed, 22 Jul 2020 15:09:13: 6000000 INFO @ Wed, 22 Jul 2020 15:09:18: 2000000 INFO @ Wed, 22 Jul 2020 15:09:18: #1 tag size is determined as 75 bps INFO @ Wed, 22 Jul 2020 15:09:18: #1 tag size = 75 INFO @ Wed, 22 Jul 2020 15:09:18: #1 total tags in treatment: 3235928 INFO @ Wed, 22 Jul 2020 15:09:18: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 15:09:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 15:09:18: #1 tags after filtering in treatment: 2548416 INFO @ Wed, 22 Jul 2020 15:09:18: #1 Redundant rate of treatment: 0.21 INFO @ Wed, 22 Jul 2020 15:09:18: #1 finished! INFO @ Wed, 22 Jul 2020 15:09:18: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 15:09:18: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 15:09:18: #2 number of paired peaks: 33 WARNING @ Wed, 22 Jul 2020 15:09:18: Too few paired peaks (33) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Wed, 22 Jul 2020 15:09:18: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8462198/SRX8462198.05_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8462198/SRX8462198.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8462198/SRX8462198.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8462198/SRX8462198.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 15:09:24: 3000000 INFO @ Wed, 22 Jul 2020 15:09:30: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Jul 2020 15:09:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8462198/SRX8462198.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8462198/SRX8462198.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8462198/SRX8462198.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8462198/SRX8462198.bam'] # control file = None # effective genome size = 1.21e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Wed, 22 Jul 2020 15:09:33: #1 read tag files... INFO @ Wed, 22 Jul 2020 15:09:33: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 15:09:37: 5000000 INFO @ Wed, 22 Jul 2020 15:09:41: 1000000 INFO @ Wed, 22 Jul 2020 15:09:45: 6000000 INFO @ Wed, 22 Jul 2020 15:09:49: 2000000 INFO @ Wed, 22 Jul 2020 15:09:50: #1 tag size is determined as 75 bps INFO @ Wed, 22 Jul 2020 15:09:50: #1 tag size = 75 INFO @ Wed, 22 Jul 2020 15:09:50: #1 total tags in treatment: 3235928 INFO @ Wed, 22 Jul 2020 15:09:50: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 15:09:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 15:09:50: #1 tags after filtering in treatment: 2548416 INFO @ Wed, 22 Jul 2020 15:09:50: #1 Redundant rate of treatment: 0.21 INFO @ Wed, 22 Jul 2020 15:09:50: #1 finished! INFO @ Wed, 22 Jul 2020 15:09:50: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 15:09:50: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 15:09:50: #2 number of paired peaks: 33 WARNING @ Wed, 22 Jul 2020 15:09:50: Too few paired peaks (33) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Wed, 22 Jul 2020 15:09:50: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8462198/SRX8462198.10_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8462198/SRX8462198.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8462198/SRX8462198.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8462198/SRX8462198.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 15:09:55: 3000000 INFO @ Wed, 22 Jul 2020 15:10:02: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Jul 2020 15:10:08: 5000000 BigWig に変換しました。 INFO @ Wed, 22 Jul 2020 15:10:15: 6000000 INFO @ Wed, 22 Jul 2020 15:10:19: #1 tag size is determined as 75 bps INFO @ Wed, 22 Jul 2020 15:10:19: #1 tag size = 75 INFO @ Wed, 22 Jul 2020 15:10:19: #1 total tags in treatment: 3235928 INFO @ Wed, 22 Jul 2020 15:10:19: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 15:10:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 15:10:19: #1 tags after filtering in treatment: 2548416 INFO @ Wed, 22 Jul 2020 15:10:19: #1 Redundant rate of treatment: 0.21 INFO @ Wed, 22 Jul 2020 15:10:19: #1 finished! INFO @ Wed, 22 Jul 2020 15:10:19: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 15:10:19: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 15:10:19: #2 number of paired peaks: 33 WARNING @ Wed, 22 Jul 2020 15:10:19: Too few paired peaks (33) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Wed, 22 Jul 2020 15:10:19: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8462198/SRX8462198.20_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8462198/SRX8462198.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8462198/SRX8462198.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8462198/SRX8462198.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling